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The repertoire of mutational signatures in human cancer (vol 578, pg 94, 2020)

NATURE 2023年第7948期614卷 E41-E41页

作者： Alexandrov, Ludmil B. Kim, Jaegil Haradhvala, Nicholas J. Huang, Mi Ni Ng, Alvin Wei Tian Wu, Yang Boot, Arnoud Covington, Kyle R. Gordenin, Dmitry A. Bergstrom, Erik N. Islam, S. M. Ashiqul Lopez-Bigas, Nuria Klimczak, Leszek J. McPherson, John R. Morganella, Sandro Sabarinathan, Radhakrishnan Wheeler, David A. Mustonen, Ville Getz, Gad Rozen, Steven G. Stratton, Michael R. Department of Cellular and Molecular Medicine Department of Bioengineering Moores Cancer Center University of California San Diego CA USA Wellcome Sanger Institute Wellcome Genome Campus Hinxton UK Department of Cellular and Molecular Medicine and Department of Bioengineering University of California San Diego La Jolla CA USA UC San Diego Moores Cancer Center San Diego CA USA University of California San Diego San Diego CA USA Broad Institute of MIT and Harvard Cambridge MA USA Center for Cancer Research Massachusetts General Hospital Boston MA USA Massachusetts General Hospital Boston MA USA Department of Pathology Massachusetts General Hospital Boston MA USA Harvard Medical School Boston MA USA Laboratory for Medical Science Mathematics RIKEN Center for Integrative Medical Sciences Yokohama Japan Computational Biology Program Ontario Institute for Cancer Research Toronto ON Canada Programme in Cancer & Stem Cell Biology Duke-NUS Medical School Singapore Singapore Centre for Computational Biology Duke-NUS Medical School Singapore Singapore Programme in Cancer and Stem Cell Biology Duke-NUS Medical School Singapore Singapore Programme in Cancer and Stem Cell Biology Centre for Computational Biology Duke-NUS Medical School Singapore Singapore SingHealth Duke-NUS Institute of Precision Medicine National Heart Centre Singapore Singapore Singapore Cancer Science Institute of Singapore National University of Singapore Singapore Singapore Institute of Molecular and Cell Biology Singapore Singapore Laboratory of Cancer Epigenome Division of Medical Science National Cancer Centre Singapore Singapore Singapore Duke-NUS Medical School Singapore Singapore Human Genome Sequencing Center Baylor College of Medicine Houston TX USA Dan L. Duncan Cancer Center Baylor College of Medicine Houston TX USA Department of Molecular and Human Genetics Baylor College of Medicine Houston TX USA Genome Integrity and Structural Biology Laboratory National Ins

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Manifold learning for organizing unstructured sets of process observations

arXiv

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arXiv 2018年

作者： Dietrich, Felix Kooshkbaghi, Mahdi Bollt, Erik M. Kevrekidis, Ioannis G. Department of Chemical and Biomolecular Engineering Department of Applied Mathematics and Statistics Johns Hopkins University BaltimoreMD21218 United States Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States Department of Mathematics Department of Electrical and Computer Engineering Clarkson Center for Complex Systems Science Clarkson University PotsdamNY13699-5815 United States

Data mining is routinely used to organize ensembles of short temporal observations so as to reconstruct useful, low-dimensional realizations of an underlying dynamical system. In this paper, we use manifold learning to organize unstructured ensembles of observations ("trials") of a system's response surface. We have no control over where every trial starts;and during each trial operating conditions are varied by turning "agnostic" knobs, which change system parameters in a systematic but unknown way. As one (or more) knobs "turn" we record (possibly partial) observations of the system response. We demonstrate how such partial and disorganized observation ensembles can be integrated into coherent response surfaces whose dimension and parametrization can be systematically recovered in a data-driven fashion. The approach can be justified through the Whitney and Takens embedding theorems, allowing reconstruction of manifolds/attractors through different types of observations. We demonstrate our approach by organizing unstructured observations of response surfaces, including the reconstruction of a cusp bifurcation surface for Hydrogen combustion in a Continuous Stirred Tank Reactor. Finally, we demonstrate how this observation-based reconstruction naturally leads to informative transport maps between input parameter space and output/state variable *** codes 37M20 Copyright © 2018, The Authors. All rights reserved.

关键词： Dynamical systems

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Assessing Trustworthy AI in Times of COVID-19: Deep Learning for Predicting a Multiregional Score Conveying the Degree of Lung Compromise in COVID-19 Patients

IEEE Transactions on Technology and Society

引用

IEEE Transactions on Technology and Society 2022年第4期3卷 272-289页

作者： Allahabadi, Himanshi Amann, Julia Balot, Isabelle Beretta, Andrea Binkley, Charles Bozenhard, Jonas Bruneault, Frederick Brusseau, James Candemir, Sema Cappellini, Luca Alessandro Chakraborty, Subrata Cherciu, Nicoleta Cociancig, Christina Coffee, Megan Ek, Irene Espinosa-Leal, Leonardo Farina, Davide Fieux-Castagnet, Genevieve Frauenfelder, Thomas Gallucci, Alessio Giuliani, Guya Golda, Adam Van Halem, Irmhild Hildt, Elisabeth Holm, Sune Kararigas, Georgios Krier, Sebastien A. Kuhne, Ulrich Lizzi, Francesca Madai, Vince I. Markus, Aniek F. Masis, Serg Mathez, Emilie Wiinblad Mureddu, Francesco Neri, Emanuele Osika, Walter Ozols, Matiss Panigutti, Cecilia Parent, Brendan Pratesi, Francesca Moreno-Sanchez, Pedro A. Sartor, Giovanni Savardi, Mattia Signoroni, Alberto Sormunen, Hanna-Maria Spezzatti, Andy Srivastava, Adarsh Stephansen, Annette F. Theng, Lau Bee Tithi, Jesmin Jahan Tuominen, Jarno Umbrello, Steven Vaccher, Filippo Vetter, Dennis Westerlund, Magnus Wurth, Renee Zicari, Roberto V. Ey Netherlands Enterprise Intelligence Department Amsterdam1083 HP Netherlands Eth Zurich Health Ethics and Policy Lab Department of Health Sciences and Technology Zürich8092 Switzerland Center for Diplomatic and Strategic Studies Postgraduate Studies in Diplomacy and International Relations Paris75015 France Pisa56124 Italy Hackensack Meridian Health Bioethics Center EdisonNJ08820 United States University of Oxford Faculty of Philosophy OxfordOX2 6GG United Kingdom Collège André- Laurendeau Philosophie Department MontrealQCH8N 2J4 Canada Université du Québec À Montréal École des Médias MontrealQCH2L 2C4 Canada Pace University Philosophy Department New YorkNY10038 United States The Ohio State University Wexner Medical Center Department of Radiology ColumbusOH43210 United States Humanitas Research Hospital Department of Radiology Milan20089 Italy Humanitas University Department of Biomedical Sciences Milan20089 Italy University of New England Faculty of Science Agriculture Business and Law ArmidaleNSW2351 Australia University of Technology Sydney Faculty of Engineering and Information Technology SydneyNSW2007 Australia Scuola Superiore Sant'Anna European Centre of Excellence on the Regulation of Robotics and Ai Pisa56127 Italy University of Bremen Group of Computer Architecture Bremen28359 Germany New York University Grossman School of Medicine Division of Infectious Diseases and Immunology Department of Medicine New YorkNY10016 United States Digital Institute Ai Research Section Stockholm16731 Sweden Arcada University of Applied Sciences Department of Business Management and Analytics Helsinki00550 Finland University of Brescia Radiological Sciences and Public Health Department of Medical and Surgical Specialties Brescia25121 Italy Sncf Reseau Sa Ethique Groupe La Plaine93418 France Institute of Diagnostic and Interventional Radiology University Hospital Zurich Zürich8091 Switzerland Eindhoven University of Tech

This article's main contributions are twofold: 1) to demonstrate how to apply the general European Union's High-Level Expert Group's (EU HLEG) guidelines for trustworthy AI in practice for the domain of healthcare and 2) to investigate the research question of what does 'trustworthy AI' mean at the time of the COVID-19 pandemic. To this end, we present the results of a post-hoc self-assessment to evaluate the trustworthiness of an AI system for predicting a multiregional score conveying the degree of lung compromise in COVID-19 patients, developed and verified by an interdisciplinary team with members from academia, public hospitals, and industry in time of pandemic. The AI system aims to help radiologists to estimate and communicate the severity of damage in a patient's lung from Chest X-rays. It has been experimentally deployed in the radiology department of the ASST Spedali Civili clinic in Brescia, Italy, since December 2020 during pandemic time. The methodology we have applied for our post-hoc assessment, called Z-Inspection®, uses sociotechnical scenarios to identify ethical, technical, and domain-specific issues in the use of the AI system in the context of the pandemic. © 2020 IEEE.

关键词： COVID-19

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Model reduction with memory and the machine learning of dynamical systems

arXiv

引用

arXiv 2018年

作者： Ma, Chao Wang, Jianchun Weinan, E. Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States Department of Mechanics and Aerospace Engineering Southern University of Science and Technology Shenzhen518055 China Beijing Institute of Big Data Research Beijing100871 China

The well-known Mori-Zwanzig theory tells us that model reduction leads to memory effect. For a long time, modeling the memory effect accurately and efficiently has been an important but nearly impossible task in developing a good reduced model. In this work, we explore a natural analogy between recurrent neural networks and the Mori-Zwanzig formalism to establish a systematic approach for developing reduced models with memory. Two training models-a direct training model and a dynamically coupled training model-are proposed and compared. We apply these methods to the Kuramoto-Sivashinsky equation and the Navier-Stokes equation. Numerical experiments show that the proposed method can produce reduced model with good performance on both short-term prediction and long-term statistical properties. Copyright © 2018, The Authors. All rights reserved.

关键词： Recurrent neural networks

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Hyperuniformity of generalized random organization models

arXiv

引用

arXiv 2018年

作者： Ma, Zheng Torquato, Salvatore Department of Physics Princeton University and Princeton New Jersey08544 United States Department of Chemistry Department of Physics Princeton Institute for the Science and Technology of Materials Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States

Studies of random organization models of monodisperse (i.e., identical) spherical particles have shown that a hyperuniform state is achievable when the system goes through an absorbing phase transition to a critical state. Here we investigate to what extent hyperuniformity is preserved when the model is generalized to particles with a size distribution and/or nonspherical shapes. We begin by examining binary disks in two dimensions and demonstrate that their critical states are hyperuniform as two-phase media, but not hyperuniform nor multihyperuniform as point patterns formed by the particle centroids. We further confirm the generality of our findings by studying particles with a continuous size distribution. Finally, to study the effect of rotational degrees of freedom, we extend our model to noncircular particles, namely, hard rectangles with various aspect ratios, including the hard-needle limit. Although these systems exhibit only short-range orientational order, hyperuniformity is still preserved. Our analysis reveals that the redistribution of the "mass" of the particles rather than the particle centroids is central to this dynamical process. The consideration of the "active volume fraction" of generalized random organization models may help to resolve which universality class they belong to and hence may lead to a deeper theoretical understanding of absorbing-state models. Our results suggest that general particle systems subject to random organization can be a robust way to fabricate a wide class of hyperuniform states of matter by tuning the structures via different particle-size and -shape distributions. This in turn potentially enables the creation of multifunctional hyperuniform materials with desirable optical, transport and mechanical properties. Copyright © 2018, The Authors. All rights reserved.

关键词： Critical current density (superconductivity)

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Precessing jet nozzle connecting to a spinning black hole in M87

arXiv

引用

arXiv 2023年

作者： Cui, Yuzhu Hada, Kazuhiro Kawashima, Tomohisa Kino, Motoki Lin, Weikang Mizuno, Yosuke Ro, Hyunwook Honma, Mareki Yi, Kunwoo Yu, Jintao Park, Jongho Jiang, Wu Shen, Zhiqiang Kravchenko, Evgeniya Algaba, Juan-Carlos Cheng, Xiaopeng Cho, Ilje Giovannini, Gabriele Giroletti, Marcello Jung, Taehyun Lu, Ru-Sen Niinuma, Kotaro Oh, Junghwan Ohsuga, Ken Sawada-Satoh, Satoko Sohn, Bong Won Takahashi, Hiroyuki R. Takamura, Mieko Tazaki, Fumie Trippe, Sascha Wajima, Kiyoaki Akiyama, Kazunori An, Tao Asada, Keiichi Buttaccio, Salvatore Byun, Do-Young Cui, Lang Hagiwara, Yoshiaki Hirota, Tomoya Hodgson, Jeffrey Kawaguchi, Noriyuki Kim, Jae-Young Lee, Sang-Sung Lee, Jee Won Lee, Jeong Ae Maccaferri, Giuseppe Melis, Andrea Melnikov, Alexey Migoni, Carlo Oh, Se-Jin Sugiyama, Koichiro Wang, Xuezheng Zhang, Yingkang Chen, Zhong Hwang, Ju-Yeon Jung, Dong-Kyu Kim, Hyo-Ryoung Kim, Jeong-Sook Kobayashi, Hideyuki Li, Bin Li, Guanghui Li, Xiaofei Liu, Zhiyong Liu, Qinghui Liu, Xiang Oh, Chung-Sik Oyama, Tomoaki Roh, Duk-Gyoo Wang, Jinqing Wang, Na Wang, Shiqiang Xia, Bo Yan, Hao Yeom, Jae-Hwan Yonekura, Yoshinori Yuan, Jianping Zhang, Hua Zhao, Rongbing Zhong, Weiye Research Center for Intelligent Computing Platforms Zhejiang Laboratory Hangzhou311100 China Tsung-Dao Lee Institute Shanghai Jiao Tong University 520 Shengrong Road Shanghai201210 China Astronomical Science Program The Graduate University for Advanced Studies SOKENDAI 2-21-1 Osawa Mitaka Tokyo181-8588 Japan Mizusawa VLBI Observatory National Astronomical Observatory of Japan 2-12 Hoshigaoka Mizusawa Iwate Oshu023-0861 Japan Institute for Cosmic Ray Research The University of Tokyo 5-1-5 Kashiwanoha Chiba Kashiwa277-8582 Japan Kogakuin University of Technology & Engineering Academic Support Center 2665-1 Nakano-machi Hachioji Tokyo192-0015 Japan South-Western Institute For Astronomy Research Yunnan University Kunming650500 China School of Physics and Astronomy Shanghai Jiao Tong University Shanghai200240 China Institut für Theoretische Physik Goethe-Universität Frankfurt Max-von-Laue-Straße 1 Frankfurt am MainD-60438 Germany Korea Astronomy & Space Science Institute Daedeokdae-ro 776 Yuseong-gu Daejeon34055 Korea Republic of Department of Astronomy Yonsei University Yonsei-ro 50 Seodaemun-gu Seoul03722 Korea Republic of Department of Astronomy Graduate School of Science The University of Tokyo 7-3-1 Hongo Bunkyo Tokyo113-0033 Japan Department of Physics and Astronomy Seoul National University Gwanak-gu Seoul08826 Korea Republic of Department of Information Countermeasure Air Force Early Warning Academy Wuhan430019 China Institute of Astronomy and Astrophysics Academia Sinica HiloHI96720 United States Shanghai Astronomical Observatory Chinese Academy of Sciences 80 Nandan Road Shanghai200030 China Key Laboratory of Radio Astronomy Chinese Academy of Sciences Beijing100101 China Moscow Institute of Physics and Technology Dolgoprudny Institutsky per. 9 Moscow141700 Russia Lebedev Physical Institute The Russian Academy of Sciences Leninsky prospekt 53 Moscow119991 Russia Department of Physics Faculty of Science U

The nearby radio galaxy M87 offers a unique opportunity to explore the connections between the central supermassive black hole and relativistic jets. Previous studies of the inner region of M87 revealed a wide opening angle for the jet originating near the black hole 1–4. The Event Horizon Telescope resolved the central radio source and found an asymmetric ring structure consistent with expectations from General Relativity 5. With a baseline of 17 years of observations, there was a shift in the jet’s transverse position, possibly arising from an eight to ten-year quasi-periodicity 3. However, the origin of this sideways shift remains unclear. Here we report an analysis of radio observations over 22 years that suggests a period of about 11 years in the position angle variation of the jet. We infer that we are seeing a spinning black hole that induces the Lense-Thirring precession of a misaligned accretion disk. Similar jet precession may commonly occur in other active galactic nuclei but has been challenging to detect owing to the small magnitude and long period of the variation. Copyright © 2023, The Authors. All rights reserved.

关键词： Active Galactic Nuclei

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The Extended [CII] under Construction? Observation of the brightest high-z lensed star-forming galaxy at z = 6.2

arXiv

引用

arXiv 2023年

作者： Fudamoto, Yoshinobu Inoue, Akio K. Coe, Dan Welch, Brian Acebron, Ana Ricotti, Massimo Mandelker, Nir Windhorst, Rogier A. Xu, Xinfeng Sugahara, Yuma Bauer, Franz E. Bradač, Maruša Bradley, Larry D. Diego, Jose M. Florian, Michael Frye, Brenda Fujimoto, Seiji Hashimoto, Takuya Henry, Alaina Mahler, Guillaume Oesch, Pascal A. Ravindranath, Swara Rigby, Jane Sharon, Keren Strait, Victoria Tamura, Yoichi Trenti, Michele Vanzella, Eros Zackrisson, Erik Zitrin, Adi Waseda Research Institute for Science and Engineering Faculty of Science and Engineering Waseda University 3-4-1 Okubo Shinjuku Tokyo169-8555 Japan National Astronomical Observatory of Japan 2-21-1 Osawa Mitaka Tokyo Japan Department of Physics School of Advanced Science and Engineering Faculty of Science and Engineering Waseda University 3-4-1 Okubo Shinjuku Tokyo169-8555 Japan 3700 San Martin Drive BaltimoreMD21218 United States STScI BaltimoreMD United States Center for Astrophysical Sciences Department of Physics and Astronomy The Johns Hopkins University 3400 N Charles St. BaltimoreMD21218 United States Department of Astronomy University of Maryland College ParkMD20742 United States Observational Cosmology Lab NASA Goddard Space Flight Center GreenbeltMD20771 United States Center for Research and Exploration in Space Science and Technology NASA/GSFC GreenbeltMD20771 United States Dipartimento di Fisica Università degli Studi di Milano Via Celoria 16 MilanoI-20133 Italy INAF - IASF Milano via A. Corti 12 MilanoI-20133 Italy Department of Astronomy University of Maryland College Park20742 United States Centre for Astrophysics and Planetary Science Racah Institute of Physics The Hebrew University Jerusalem91904 Israel School of Earth and Space Exploration Arizona State University TempeAZ85287-1404 United States Center for Astrophysical Sciences Department of Physics & Astronomy Johns Hopkins University BaltimoreMD21218 United States Instituto de Astrofísica Facultad de Física Pontificia Universidad Católica de Chile Campus San Joaquín Av. Vicuña Mackenna 4860 Macul Santiago7820436 Chile Centro de Astroingeniería Facultad de Física Pontificia Universidad Católica de Chile Campus San Joaquín Av. Vicuña Mackenna 4860 Macul Santiago7820436 Chile Millennium Institute of Astrophysics Nuncio Monseñor Sótero Sanz 100 Of 104 Providencia Santiago Chile University of Ljubljana Department of Mathematics and Physics Jad

We present results of [C ii] 158 µm emission line observations, and report the spectroscopic redshift confirmation of a strongly lensed (µ ∼ 20) star-forming galaxy, MACS0308-zD1 at z = 6.2078 ±0.0002. The [C ii] emission line is detected with a signal-to-noise ratio > 6 within the rest-frame UV bright clump of the lensed galaxy (zD1.1) and exhibits multiple velocity components;the narrow [C ii] has a velocity full-width-half-maximum (FWHM) of 110 ± 20 km/s, while broader [C ii] is seen with an FWHM of 230 ± 20 km/s. The broader [C ii] component is blueshifted (−80 ± 20 km/s) with respect to the narrow [C ii] component, and has a morphology which extends beyond the UV-bright clump. We find that while the narrow [C ii] emission is most likely associated with zD1.1, the broader component is possibly associated with outflowing gas. Based on the non-detection of λ158 µm dust continuum, we find that MACS0308-zD1’s star-formation activity occurs in a dust-free environment with the stringent upper limit of infrared luminosity . 9 × 108 L•. Targeting this strongly lensed faint galaxy for followup ALMA and JWST observations will be crucial to characterize the details of typical galaxy growth in the early Universe. © 2023, CC BY.

关键词： Galaxies

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Uncovering multiscale order in the prime numbers via scattering

arXiv

引用

arXiv 2018年

作者： Torquato, .S. Zhang, .G. De Courcy-Ireland, M. Department of Chemistry Department of Physics Princeton Institute for the Science and Technology of Materials Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 Department of Chemistry Princeton University PrincetonNJ08544 United States Department of Mathematics Princeton University PrincetonNJ08544 United States

The prime numbers have been a source of fascination for millenia and continue to surprise us. Motivated by the hyperuniformity concept, which has attracted recent attention in physics and materials science, we show that the prime numbers in certain large intervals possess unanticipated order across length scales and represent the first example of a new class of many-particle systems with pure point diffraction patterns, which we call effectively limit-periodic. In particular, the primes in this regime are hyperuniform. This is shown analytically using the structure factor S(k), proportional to the scattering intensity from a many-particle system. Remarkably, the structure factor for primes is characterized by dense Bragg peaks, like a quasicrystal, but positioned at certain rational wavenumbers, like a limit-periodic point pattern. We identify a transition between ordered and disordered prime regimes that depends on the intervals studied. Our analysis leads to an algorithm that enables one to predict primes with high accuracy. Effective limit-periodicity deserves future investigation in physics, independent of its link to the primes. Copyright © 2018, The Authors. All rights reserved.

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HIDDEN MULTISCALE ORDER IN THE PRIMES

arXiv

引用

arXiv 2018年

作者： Torquato, Salvatore Zhang, Ge Courcy-Ireland, Matthew De Department of Chemistry Department of Physics Princeton Institute for the Science and Technology of Materials Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 Department of Chemistry Princeton University PrincetonNJ08544 United States Department of Mathematics Princeton University PrincetonNJ08544 United States

We study the pair correlations between prime numbers in an interval M ≤ p ≤ M + L with M → ∞, L/M → β > 0. By analyzing the structure factor, we prove, conditionally on the Hardy-Littlewood conjecture on prime pairs, that the primes are characterized by unanticipated multiscale order. Specifically, their limiting structure factor is that of a union of an infinite number of periodic systems and is characterized by dense set of Dirac delta functions. Primes in dyadic intervals are the first examples of what we call effectively limit-periodic point configurations. This behavior implies anomalously suppressed density fluctuations compared to uncorrelated (Poisson) systems at large length scales, which is now known as hyperuniformity. Using a scalar order metric τ calculated from the structure factor, we identify a transition between the order exhibited when L is comparable to M and the uncorrelated behavior when L is only logarithmic in M. Our analysis for the structure factor leads to an algorithm to reconstruct primes in a dyadic interval with high accuracy. Copyright © 2018, The Authors. All rights reserved.

关键词： Delta functions

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Nonlinear Landau-Zener-Stückelberg-Majorana interferometry

引用

Physical Review A 2018年第1期98卷 013601-013601页

作者： Sheng-Chang Li Li-Bin Fu Jie Liu School of Science Xi'an Jiaotong University Xi'an 710049 China and Shaanxi Province Key Laboratory of Quantum Information and Quantum Optoelectronic Devices Xi'an Jiaotong University Xi'an 710049 China Graduate School China Academy of Engineering Physics Beijing 100193 China HEDPS CAPT and CICIFSA MoE Peking University Beijing 100871 China Laboratory of Computational Physics Institute of Applied Physics and Computational Mathematics Beijing 100088 China

We investigate Landau-Zener-Stückelberg-Majorana (LZSM) interferometry in a nonlinear two-level system subjected to a sinusoidal driving field. A comprehensive analysis for the interference patterns is shown from which we can analytically obtain the condition of constructive and destructive interferences in some cases. In the presence of nonlinear interaction, the level structure is changed, which can lead to an asymmetric deformation of the interference patterns and a significant position shift of the interference fringes. Our findings suggest an application of the nonlinear LZSM interferometry in accurately calibrating the parameters characterizing a nonlinear two-level system, as well as its coupling with the driven fields.

关键词： Bose-Einstein condensates Quantum control Quantum interference effects Ultracold gases

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